Veno-venous collaterals are sometimes seen in patients after the Fontan procedure. A 28-year-old female with tricuspid atresia who underwent the Fontan procedure had oxygen desaturation due to a giant veno-venous collateral. Coil embolization was performed for the collateral. After the procedure, she complained of severe back pain. Anti-inflammatory analgesics and steroids were not effective, although carbamazepine promptly relieved the intractable pain. Treatment-related pain after coil embolization for veno-venous collaterals in patients with Fontan physiology is quite rare, although cardiologists must recognize a critical condition to be differentiated from vascular occlusion.